Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

[Background] The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. In this study, a sample of Indian collections together with a selection of world-wide cultivars to analyze the genetic diversity structure based on Genotype by Sequence data.

[Results] A set of 6158 informative Single Nucleotide Polymorphism (SNP) in 175 melon accessions was generated. Melon germplasm could be classified into six major groups, in concordance with horticultural groups. Indian group was in the center of the diversity plot, with the highest genetic diversity. No strict genetic differentiation between wild and cultivated accessions was appreciated in this group. Genomic regions likely involved in the process of diversification were also found. Interestingly, some SNPs differentiating inodorus and cantalupensis groups are linked to Quantitiative Trait Loci involved in ripening behavior (a major characteristic that differentiate those groups). Linkage disequilibrium was found to be low (17 kb), with more rapid decay in euchromatic (8 kb) than heterochromatic (30 kb) regions, demonstrating that recombination events do occur within heterochromatn, although at lower frequency than in euchromatin. Concomitantly, haplotype blocks were relatively small (59 kb). Some of those haplotype blocks were found fixed in different melon groups, being therefore candidate regions that are involved in the diversification of melon cultivars.

[Conclusions] The results support the hypothesis that India is the primary center of diversity of melon, Occidental and Far-East cultivars have been developed by divergent selection. Indian germplasm is genetically distinct from African germplasm, supporting independent domestication events. The current set of traditional Indian accessions may be considered as a population rather than a standard collection of fixed landraces with high intercrossing between cultivated and wild melons.

Javier Forment from the Bioinformatics Core Service at IBMCP for support in bioinformatics analysis. We also acknowledge the support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI). NPS Dhillon was supported by long-term strategic donors to the World Vegetable Center: Republic of China (Taiwan), UK aid from the UK government, United States Agency for International Development (USAID), Australian Centre for International Agricultural Research (ACIAR), Germany, Thailand, Philippines, Korea, and Japan.This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO)-FEDER grant AGL2015–64625-C2-R to AJM (project conception, experiments, data acquisition and analysis, manuscript writing, publication costs), AGL2017–85563-C2–1-R and the PROMETEO/2017/078 grant funded by Generalitat Valenciana (Conselleria d’Educació, Investigació, Cultura i Esport) to BP (project conception, provide samples and manuscript drafting). AD was supported by a Jae-Doc contract from CSIC (experiments and manuscript drafting).